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- PDB-2glp: Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydr... -

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Basic information

Entry
Database: PDB / ID: 2glp
TitleCrystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with compound 1
Components(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
KeywordsLYASE / FabZ complex
Function / homology
Function and homology information


3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / lipid A biosynthetic process / fatty acid biosynthetic process / membrane / cytoplasm
Similarity search - Function
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-BDE / BENZAMIDINE / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsZhang, L. / Liu, W. / Shen, X. / Jiang, H.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural basis for catalytic and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ).
Authors: Zhang, L. / Liu, W. / Hu, T. / Du, L. / Luo, C. / Chen, K. / Shen, X. / Jiang, H.
History
DepositionApr 5, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (3R)-hydroxymyristoyl-acyl carrier protein dehydratase
B: (3R)-hydroxymyristoyl-acyl carrier protein dehydratase
C: (3R)-hydroxymyristoyl-acyl carrier protein dehydratase
D: (3R)-hydroxymyristoyl-acyl carrier protein dehydratase
E: (3R)-hydroxymyristoyl-acyl carrier protein dehydratase
F: (3R)-hydroxymyristoyl-acyl carrier protein dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,91424
Polymers117,6706
Non-polymers2,24418
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20380 Å2
ΔGint-132 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.003, 100.578, 186.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
(3R)-hydroxymyristoyl-acyl carrier protein dehydratase / FabZ


Mass: 19611.656 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: SS1 / Gene: FabZ / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q5G940, UniProt: O25928*PLUS, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-BDE / N'-[(1E)-(3,5-DIBROMO-2,4-DIHYDROXYPHENYL)METHYLENE]NICOTINOHYDRAZIDE


Mass: 415.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9Br2N3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1M Sodium Acetate trihydrate PH3.8, 2.0M Sodium Formate, 20%(w/v) Benzamidine HCl , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. all: 49567 / Num. obs: 48277 / % possible obs: 92.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Χ2: 1.036 / Net I/σ(I): 14.2
Reflection shellResolution: 2.42→2.51 Å / % possible obs: 87.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.72 / Num. unique all: 4663 / Num. unique obs: 4663 / Rsym value: 0.27 / Χ2: 1.053

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GLL

2gll


Resolution: 2.42→50 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4842 8.8 %RANDOM
Rwork0.189 ---
all-49567 --
obs-48277 87.4 %-
Solvent computationBsol: 40.432 Å2
Displacement parametersBiso mean: 26.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.547 Å20 Å20 Å2
2--5.289 Å20 Å2
3----5.836 Å2
Refinement stepCycle: LAST / Resolution: 2.42→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7290 0 138 538 7966
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1071.5
X-RAY DIFFRACTIONc_scbond_it1.8692
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scangle_it2.7422.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2cis_peptide.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION43041-BEN.param
X-RAY DIFFRACTION5ion.param

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